Yuanfang Guan, PhD

Guan-Yuanfan.jpg
Professor of Computational Medicine and Bioinformatics
Professor of Internal Medicine, Medical School
[email protected]
Available to mentor
Yuanfang Guan, PhD
Guan-Yuanfan.jpg
Professor
  • Qualifications
  • Research Overview
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  • Recent Publications
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  • Qualifications

    • Ph.D., Molecular Biology
      Princeton University, Princeton, NJ, United States
      2005 - 2010
    • BS, Biology
      The University of Hong Kong, Hong Kong, China
      2002 - 2005

    Research Overview

    The Guan lab's research focus is machine learning in biology and medical fields.

    Links

    • Guan Lab

    Recent Publications

    See All Publications
    • Journal Article
      PSGRN: Gene regulatory network inference from single-cell perturbational data through self-training with synthetic gold standards.
      Song X, Deng K, Chen M, Guan Y. Sci Adv, 2026 May; 12 (18): eaeb3376 DOI:10.1126/sciadv.aeb3376
      PMID: PMC13127566
    • Journal Article
      Learnable Diffusion Framework for Mouse V1 Neural Decoding.
      Deng K, Schwendeman PS, Guan Y. Adv Sci (Weinh), 2026 Mar 5; e20220 DOI:10.1002/advs.202520220
      PMID: 41787846
    • Journal Article
      Lipid Metabolism Transcriptomic Signature of Defective Erythropoiesis in Diamond Blackfan Anemia syndrome.
      Deng K, Wang Y, Min JC, Liu X, Ueharu H, Myers G, Yu L, Hammoud SB, Adam A, Saba R, Natogi V, Drysdale C, Chen B, Yee JL, Kitzman J, Lyssiotis CA, Mishina Y, Jones MA, Kaartinen V, Guan Y, Khoriaty R, Engel JD, Singh SA. Blood Adv, 2026 Jan 23; DOI:10.1182/bloodadvances.2025017318
      PMID: 41576344
    • Journal Article
      ImageDoubler: image-based doublet identification in single-cell sequencing
      Deng K, Xu X, Zhou M, Li H, Keller ET, Shelley G, Lu A, Garmire L, Guan Y. Nature Communications, 2025 Dec 1; 16 (1): DOI:10.1038/s41467-024-55434-0
      PMID: 39747095
    • Journal Article
      Publisher Correction: The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles (Genome Biology, (2023), 24, 1, (79), 10.1186/s13059-023-02915-y)
      Schreiber JM, Boix CA, wook Lee J, Li H, Guan Y, Chang CC, Chang JC, Hawkins-Hooker A, Schölkopf B, Schweikert G, Carulla MR, Canakoglu A, Guzzo F, Nanni L, Masseroli M, Carman MJ, Pinoli P, Hong C, Yip KY, Spence JP, Batra SS, Song YS, Mahony S, Zhang Z, Tan W, Shen Y, Sun Y, Shi M, Adrian J, Sandstrom RS, Farrell NP, Halow JM, Lee K, Jiang L, Yang X, Epstein CB, Strattan JS, Bernstein BE, Snyder MP, Kellis M, Noble WS, Kundaje AB. Genome Biology, 2025 Dec 1; 26 (1): DOI:10.1186/s13059-025-03494-w
      PMID: 39948633
    • Preprint
      GRASP: Gene-Relation Adaptive Soft Prompt for Universal Gene Network Inference
      Feng Y, Deng K, Guan Y. 2025 Oct 23; bioRxiv, DOI:10.1101/2025.10.20.683485
    • Journal Article
      Accelerating Cough-Based Algorithms for Pulmonary Tuberculosis Screening: Results From the CODA TB DREAM Challenge
      Jaganath D, Sieberts SK, Raberahona M, Huddart S, Omberg L, Rakotoarivelo R, Lyimo I, Lweno O, Christopher DJ, Nhung NV, Worodria W, Yu C, Chen JY, Chen SH, Chen TM, Huang CH, Huang KL, Mulier F, Rafter D, Shih ESC, Tsao Y, Wang HK, Wu CH, Bachman C, Burkot S, Dewan P, Kulhare S, Small PM, Yadav V, Grandjean Lapierre S, Theron G, Cattamanchi A, Ahuja G, Balodi S, Khurdiya D, Kutum R, Rao AM, Salampuria A, Akbarian S, Asgarian S, Arora A, Choudhury S, Raghava GPS, Dong S, Guan Y, Nan Y, Zhang H, Gupta A, Li T, Singh R, Jeon J, Jetha Q, Lu Z, Patiyal S, Suda C. Open Forum Infectious Diseases, 2025 Oct 1; 12 (10): DOI:10.1093/ofid/ofaf572
    • Journal Article
      A community effort to optimize sequence-based deep learning models of gene regulation
      Rafi AM, Nogina D, Penzar D, Lee D, Lee D, Kim N, Kim S, Kim D, Shin Y, Kwak IY, Meshcheryakov G, Lando A, Zinkevich A, Kim BC, Lee J, Kang T, Vaishnav ED, Yadollahpour P, AiWei Y, JingZhe W, JiaXing C, Schmitz C, Salomone R, Perrin D, Bradford J, Kumar S P, Gupta K, Palaniappan A, Malousi A, Kyriakidis K, Kardamiliotis K, Emrich S, Babjac A, Queen O, Lu Z, Madsen J, Kavaliauskaite G, Møller A, Soylemez O, Schubach M, Dash PM, Röner S, Li Y, Brors B, Feuerbach L, Körner C, Abad N, Wan C, Barton C, Greaves P, Alsaggaf I, Huang KL, Chen JY, Wu CH, Chen SH, Shih ESC, Wang HK, Huang CH, Chen TM, Takatsu M, Hiratsuka Y, Davuluri RV, Liu H, Ji Y, Surana P, Sathian R, Dutta P, Zhou Z, Wen J, Dixit G, Ding K, Yang Y, Chen K, Ding M, Guan Y, Tinti M, Jones DT, Chen X, Koo P, Narayanan A, Prakash A, Labelson E, Yu Y, Ghotra R, Qiu W, Zhang W, Tu X, Nguyen T, Tran D, Trapotsi MA, Svensson F, Bornelöv S, Kim S, Albrecht J, Regev A, Gong W, Kulakovskiy IV, Meyer P, de Boer CG. Nature Biotechnology, 2025 Aug 1; 43 (8): 1373 - 1383. DOI:10.1038/s41587-024-02414-w
      PMID: 39394483

    Featured News & Stories

    Photos of DCMB promoted faculty: Yuanfang Guan, Ph.D., Jie Liu, Ph.D., Ryan Mills, Ph.D., Stephen C.J. Parker, Ph.D., and Arvind Rao, Ph.D.
    Department News

    Five DCMB faculty are promoted, congratulations!

    Five DCMB faculty were promoted. They are Yuanfang Guan, Ph.D., Jie Liu, Ph.D., Ryan Mills, Ph.D., Stephen C.J. Parker, Ph.D., and Arvind Rao, Ph.D. Congratulations!